ES4 -- Microbial Soil Community Profiling of Grace Street Park Outer Walking Paths in Greenwood, South Carolina through Illumina MiSeq Sequencing
Start Date
8-4-2022 10:30 AM
End Date
8-4-2022 12:15 PM
Location
URC Greatroom
Document Type
Event
Abstract
City parks and urban environments contain unique microbiomes due to human and animal activities unique to these areas. Bioactive microorganisms are mostly found in the top few inches of soil which often contains polluted material, agricultural products, and animal waste products. These materials provide selective pressures on the microorganisms that exist there. Generally, areas with increasing population densities have increased pollution and waste (Ferreira et al. 2018). According to a study by Delgado-Baquerizo et al. (2021), microbes inhabiting city parts and gardens in densely populated cities are exhibiting a higher proportion of key antibiotic resistance genes. After a brief literature review, we found little to no research on the biodiversity and bioactivity of microorganisms in recreational parks. Soil samples were taken in Grace Street Park in Greenwood, South Carolina. DNA was extracted from 2.5g of soil using Quiagen DNeasy PowerSoil Pro Kit following the standard manufacturer's protocol. Concentrations of extracted DNA were assessed using a Nanodrop spectrophotometer to ensure successful DNA extraction and quantification for sequence library preparation. DNA samples were sent to University of Michigan’s Microbiome Core (Ann Arbor, MI) for library preparation and next generation sequencing. The V4 region of the 16S rRNA gene was amplified for downstream sequencing with the commonly used primers 16Sf-V4 (515f) and 16Sr-V4 (806r) and a previously developed protocol (Caporaso et al. 2012; Kozich et al. 2013). Sequencing was accomplished via a MiSeq high-throughput sequencer (Illumina, San Diego, CA). Acquired DNA sequences were filtered for quality and analyzed using MOTHUR v 1.47.0 (Schloss et al. 2009) following the MiSeq SOP (available at https://www.mothur.org/) with modifications. This study has provided an initial characterization of microbial communities collected along the outer walking paths of Grace Street Park in Greenwood, South Carolina.
Keywords
Ecological Science
ES4 -- Microbial Soil Community Profiling of Grace Street Park Outer Walking Paths in Greenwood, South Carolina through Illumina MiSeq Sequencing
URC Greatroom
City parks and urban environments contain unique microbiomes due to human and animal activities unique to these areas. Bioactive microorganisms are mostly found in the top few inches of soil which often contains polluted material, agricultural products, and animal waste products. These materials provide selective pressures on the microorganisms that exist there. Generally, areas with increasing population densities have increased pollution and waste (Ferreira et al. 2018). According to a study by Delgado-Baquerizo et al. (2021), microbes inhabiting city parts and gardens in densely populated cities are exhibiting a higher proportion of key antibiotic resistance genes. After a brief literature review, we found little to no research on the biodiversity and bioactivity of microorganisms in recreational parks. Soil samples were taken in Grace Street Park in Greenwood, South Carolina. DNA was extracted from 2.5g of soil using Quiagen DNeasy PowerSoil Pro Kit following the standard manufacturer's protocol. Concentrations of extracted DNA were assessed using a Nanodrop spectrophotometer to ensure successful DNA extraction and quantification for sequence library preparation. DNA samples were sent to University of Michigan’s Microbiome Core (Ann Arbor, MI) for library preparation and next generation sequencing. The V4 region of the 16S rRNA gene was amplified for downstream sequencing with the commonly used primers 16Sf-V4 (515f) and 16Sr-V4 (806r) and a previously developed protocol (Caporaso et al. 2012; Kozich et al. 2013). Sequencing was accomplished via a MiSeq high-throughput sequencer (Illumina, San Diego, CA). Acquired DNA sequences were filtered for quality and analyzed using MOTHUR v 1.47.0 (Schloss et al. 2009) following the MiSeq SOP (available at https://www.mothur.org/) with modifications. This study has provided an initial characterization of microbial communities collected along the outer walking paths of Grace Street Park in Greenwood, South Carolina.